Alkaline stress has serious negative effects on citrus production. Ziyang xiangcheng (Citrus junos Sieb. ex Tanaka) (Cj) has been reported to be a rootstock that is tolerant to alkaline stress and iron deficiency. Poncirus trifoliata (Poncirus trifoliata (L.) Raf.) (Pt), the most widely used rootstock in China, is sensitive to alkaline stress. To investigate the molecular mechanism underlying the tolerance of Cj to alkaline stress, next-generation sequencing was employed to profile the root transcriptomes and small RNAs of Cj and Pt seedlings which were cultured in nutrient solution with three gradient pH. This two-regulation level data set provides a system-level view of molecular events with precise resolution. The data suggest that the auxin pathway may play a central role in inhibitory effect of alkaline stress on root growth, and the regulation of auxin homeostasis under alkaline stress was important for citrus adapting to alkaline stress. Moreover, the JA pathway shown an opposite response to alkaline stress in Cj and Pt may contributes to the differentials of root system architecture and iron deficiency tolerance between Cj and Pt. The data set provides a wealth of genomic resources and new clues for further studying the mechanisms underlying Cj that resist alkaline stress.
Overall design: The seeds of Cj and Pt were surface-sterilized and their germination accelerated. The seedlings were grown in a growth chamber until they had four leaves. Then, the seedlings were selected by uniform size and transferred into hydroponics with 4 L solution in a green house. Three different pH gradients (6.5, 8.0 and 9.5) were set up. Because most natural soils have a weak acidity, we set pH 6.5 as the normal condition. After 8 weeks of culture, three biological replicates (three seedling plants per replicate) were harvested randomly for each treatment. Cj1, Cj2 and Cj3 were represented the seedlings of Cj cultured in pH 6.5, 8.0 and 9.5 condition, respectively. And it was the same for naming the seedlings of Pt. The root tissues of Cj and Pt were used for RNA-seq. A total of six different samples, each with three replicates, were used for RNA-seq.
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